Functional similarity of Knirps CtBP-dependent and CtBP-independent transcriptional repressor activities

Short-range transcriptional repressors are locally acting factors that play important roles in developmental gene expression in Drosophila. To effect repression, Knirps and other short-range repressors bind the CtBP corepressor, but these repressors also function via CtBP-independent pathways. Possible mechanistic differences between CtBP-dependent and -independent repression activities are poorly understood. The distinct activities might provide qualitatively different activities necessary in different promoter contexts, or they might combine to give quantitatively different effects. We analyze separately the CtBP-dependent and CtBP-independent domains of Knirps previously characterized in the embryo to determine possible functional distinctions of the two repression activities. Both domains are active in cell culture and are dependent on the same residues required for activity in the embryo. The domains have similar properties with respect to distance-dependent repression and resistance to inhibition by the deacetylase inhibitor trichostatin A. In tests of repressor-activator specificity, the extent of repression was related not to the chemical nature of the activation domain but to the total activation potential. This result indicates that the balance of competing activation and repression signals is decisive in determining the effectiveness of repressors on genetic switches, suggesting that multiple repression activities are utilized to provide quantitatively, rather than qualitatively, distinct outputs.